Operation SNAFU
by mellra
Summary: The war against the Covenant is going badly, with humanity on the brink of destruction. In desperation, ONI turns to one scientist with fewer morals than Halsey. Orochimaru will show them that the best weapon is the one you don't see coming. Challenge fic.


**Operation: SNAFU**

 **AN:** Here is an original Naruto/Halo challenge for you all that is also a birthday gift to my friend Dimension Distorter who loved the concept of this story. Ok, so during the war (like 10 years before the first Halo game), a scientist for ONI named Orochimaru who was a rival of Dr. Halsey (seriously, how many rivals did that bitch have?) who was working on alternative methods to end the Human/Covenant War. Orochimaru has even fewer morals than Halsey, and thinks of the perfect spy/soldier to create. Taking several children, Orochimaru uses his knowledge of biology and the latest genetic technology to splice different members of the Covenant DNA with that of the children's. Out of all them, only one survives the procedure; a five year old orphan named Naruto Uzumaki, otherwise known as Subject 09. Naruto can take on the form of most of the Covenant's species and has their strengths. The only exceptions to this are Hunters (since they're a hive species) and Prophets (Orochimaru was unable to obtain a DNA sample from them). Naruto would be trained over the years to be the perfect spy and soldier, infiltrating the Covenant's ranks by age twelve with his Smart AI Kurama. Naruto will relay important military information to the UNSC that will lead to several victories over the Covenant. Though during this time, Naruto will remember what his parents (who were secretly killed by ONI for interfering with their work) would tell him about trying to find peace between the species. He'll then make it his personal mission to try to find a peaceful solution to end the war, while trying not to blow his cover and not get killed by marines (or a certain 'Demon') along the way.

Again this will be a _**CHALLENGE**_ , so unless I say otherwise this will not be continued by me only by whoever adopts it. Please inform your friends who might be interested, or even give it a try yourself! Anyway, on to the show.

 **Year 2542 (Ten Years before the events of Halo)**

Margaret Parangosky, head of the Office of Naval Intelligence (ONI) scowled as she stepped off her Pelican transport. Her sour mood could be contributed to the fact that humanity's war with the alien race, the Covenant, was going poorly as more and more of the colonies burned. It could also be due to the fact that public opinion of the UNSC was at an all-time low, and if (when she mentally corrected herself) the Covenant were finally defeated, the chances of another Insurrection breaking out were increasing all the time. But the real reason the nearly 90 year old woman looked like she just stepped in dog shit was more due to the person (and she used the term loosely) she was going to visit today.

'It can't be helped,' she mentally told herself. 'That man is one of the few near Halsey's level of intellect. If anyone has come up with a way for us to win this war, it's him. God help me.'

Steeling herself, she went into the private research facility that was built not too far from where the original Spartan II's were trained. Ignoring all the scientists and researchers bustling around her, Parangosky went straight to the express elevator located in the back of the main lobby. Once there, she placed her eyes in front of the retinal scanner and the elevator suddenly shot downwards to the underground bunker the building was built on top of. After she exited the building, she hid her cringe of disgust and fear at the room she had walked into. It looked like a mad scientist's lab from a 21st century horror movie, filled with beakers and test tubes containing a multitude of different chemicals and in some cases body parts and organs. Swallowing the bile that had risen in the back of her throat, she traveled deeper into the bunker until she saw a man with his back turned to her working at a dissection table.

"Kukuku, well isn't this a surprise. To what do I owe this unexpected visit Margaret?" a silky voice chuckled darkly from the man who had yet to turn around from whatever he was working on.

Knowing playing mind games was this man's specialty, Parangosky decided that she wouldn't give him the satisfaction and went straight to the point. "Humanity is losing this war, and I need your help. Can you do that, Orochimaru?"

The man turned and the head of ONI got a good look at the man. He was tall and slender, almost feminine in body build. Orochimaru's skin was also much too pale, a sign that he rarely left his laboratory, but he had purple tribal like markings tattooed around his yellow, snakelike eyes. With his body turned, Margaret could see the body he was dissecting, and saw that it was that of an unnamed Marine that had most likely died on the battlefield, but now looked more like a carved up piece of beef thanks to Orochimaru's 'experiments'. Said man gave a wide smirk as he brushed some of his long black hair out of his face and said in the same tone of voice, "Why of course my dear. It would be my pleasure."

At that moment, Margaret Parangosky felt as if she had just made a deal with the Devil.

 **Hours Later**

"Run that by me one more time," Parangosky said in what she hoped was a neutral voice, but failed to keep some of the disgust out of the tone if Orochimaru's widening smile was anything to go by. "You want to do WHAT?"

Orochimaru chuckled softly as he held his hands behind his back. "It's quite simple really. As you yourself have admitted, humanity's attempts at a frontal war with the Covenant has been less than fruitful. Even Halsey's windup toy soldiers can only do so much against an advanced alien race that seems to have a counter for every move we make. The answer for this is something ONI excels at; subterfuge. Most wars have been won thanks to the usage of Black Ops and spy networks, even if their efforts never make official records. The problem is that doing this with the Covenant is nearly impossible, as there is no real way to get a spy into their ranks. After all, no human could even get close without being shot at and the members of the Covenant are either too loyal to their cause or have been bought off by them, so convincing any of the members to become a turncoat would be foolhardy. That's where my plan comes in."

"You want to… _make_ …your own Covenant?" Parangosky asked, this time not even bothering to hide her disgust. "And how, pray tell, to you intend to do _that_? Clone some?"

Orochimaru waved his hand in a dismissive gesture. "Oh no, nothing like that. You know as well as I do that the cloning process is faulty at best, and even if it worked perfectly there is the factor of whether the clones would be loyal to us plus the time it would take to raise them effectively. No, my plan has a greater percentage of success."

Getting a bad feeling, Parangosky inquired, "And what is your plan?"

Orochimaru smiled even further if that was physically possible and gestured to his 'experiments' lining the walls of his lab. "You are familiar with my work on gene splicing, correct?" Seeing the woman nod he continued, "Well, I ran the variables a while ago just for fun, and I found out that human DNA is able to bind with that of most of the different Covenant species. Therefore, by using genetic manipulation, I can turn a human being into a unique hybrid between man and alien. A sort of Covenant chameleon, if you will. Then, with the right training and intel, we can send our spy into the Covenant's ranks and sow discord from within, thereby giving the UNSC the edge it needs to win!"

Parangosky looked at the pale scientist as if he'd slipped even deeper into madness. "Are you saying you'd turn a human, an already living, breathing, and thinking human, and turning them into one of the very monsters that have been killing us off for years? Are you insane?!"

Orochimaru looked at the woman, amusement dancing in his eyes. "Ah, but you see they would be neither human nor Covenant at that point my dear, but something beyond either species. If I had to compare it to anything, I would say they would almost be like a werewolf of myth but instead of turning into a wolf, they could turn into a member of the Covenant. Think about it: with the right manipulations, you could have them pull off assassinations, discover information that not even AIs can reach, and foil battle plans to ensure human victory! I've known you for a long time, Margaret. Surely a practical person such as yourself can see the benefits to this."

The small, barely living portion of Margaret Parangosky's morality rebelled with every fiber of its being against this plan. It went against every moral code to science and humanity in general, and if it was found out she approved of this to the higher brass, then burning her at the stake would be a mercy compared to what they'd do to her. However, the cold, logical portion of her that had been her driving force for decades saw that the scientist had a strong point. Even with all of humanity's advances, they were still on the defensive against the Covenant and kept getting pushed back with glassed planets as a reminder for each failure. If they could get even one spy successfully into the Covenant's ranks, it could mean the difference between victory and defeat. As always, her logical portion won out.

"What would you need?" she asked in a voice filled with iron-clad resolve.

Orochimaru looked like a kid in a candy store as he began giving her a list of equipment and staff that he would require for this to work. When he came to one item, however, she stopped him.

"Why do you need children as test subjects?" she very nearly spat out, thinking that the depravity of this man could truly go no further.

Orochimaru answered, "Children, specifically those between the ages of newborns to six year olds, have very adaptable bodies and DNA. Thus they are more likely to survive the process. Besides, if we spend a few years teaching them on the data we found on the Covenant, they are more likely to become better actors than say a soldier who had fought and hates everything about them. Of course we will need a few years, probably between five to ten, in order for them to be ready to be placed on the field. It is fortunate that the Covenant isn't above having children as soldiers as well, otherwise their age could be a detrimental factor."

Seeing the look Parangosky was giving him, Orochimaru frowned. "Now don't give me that look Margaret. You above all people know the sacrifices one must make both as a scientist and as a leader. Why else have you let Halsey and Ackerson proceed as they have? Don't bother trying to say you didn't know what they were doing when they started their Spartan programs. There isn't much that happens in the UNSC that you aren't aware of. Sure, at the end of the day you'll most likely deny it. Say that you had no idea that they were using children, kidnapped or otherwise, to become soldiers. You'll probably label us all as war criminals after this is all over anyway, but the fact is you knew and you helped. That's all there is to it."

The leader of ONI scowled. "If you know you're going to be labeled a war criminal along with Halsey and Ackerson, then why bother doing it at all?"

Orochimaru smirked, "Well you could say it is out of loyalty to humanity and the UNSC, but that would be a lie of course. The honest answer is that I find it amusing. It's almost like a game of sorts; will our sins help keep humanity alive? Will we be persecuted by the very people who we helped? It's really quite entertaining to think about. Besides, you're giving me the chance to explore my genius to its fullest capacity, so who am I to refuse?"

Orochimaru's mocking laughter followed Parangosky all the way to her Pelican.

 **One Month Later**

The head of ONI watched as Orochimaru went over the files for potential 'candidates' for what was being dubbed 'Operation: SNAFU'. It had taken some time to find children in the right age category that met all the physical and mental requirements that Orochimaru listed, but after the Spartan II's 'recruitment' program, ONI had become old pros at it. This time there was no shortage of orphans to choose from though, thanks to the Covenant's glassing of planets. The twisted scientist hummed as he scanned each folder, placing some in one pile while others he placed in another pile marked 'rejected'. He stopped, however, when he reached a file labeled Subject 09.

"Oho, what's this? I believe I recognize this child. He's Minato and Kushina's child, is he not?" he inquired, showing the picture in the file of a small blonde child with blue eyes and whisker shaped birthmarks.

Parangosky scowled but nodded and Orochimaru chuckled. "Kukuku. Interesting on how the child of two of the UNSC's most hated rivals found his way onto this list. If I didn't know any better, I'd say you were punishing the parents from beyond the grave, Margaret."

Minato and Kushina Uzumaki-Namikaze were political activists that had been doing peace work on the colonies for years. It was rumored that they had been helping the Insurrectionist factions that still existed, but no concrete evidence was to be found. If anything, the two were pacifists, trying to prevent conflict wherever they went. They were even making plans on how the colonists could peacefully break free from UNSC control after the war, and had even been talking about trying to find sympathetic members of the Covenant to end the war with as little bloodshed as possible. They were dreamers in Parangosky's opinion. Dangerous dreamers who had been gathering way too much support to be considered a minor nuisance. That was why ONI had arranged an…'accident' for the couples' off world transport nearly six months ago, but their son survived due to visiting a friend of the family at the time. Parangosky actually just wanted the boy to vanish into obscurity like his parents did, but it seemed fate had other plans because the child had met all of Orochimaru's requirements.

"Don't look too hard into it, Orochimaru," Parangosky snapped, "Now shut up and continue."

"Very well," Orochimaru said airily before going back to the files, though the woman noticed he kept Subject 09's folder separate from the rest like he was keeping a close eye on it.

 **Two Years Later**

Orochimaru was standing on an observation deck that viewed a simulated open field where thirteen figures stood. Twelve of the figures were members of the research facilities security team while the last was that of a seven year old blonde child. They were all standing still as if waiting for some unknown signal. Suddenly, Orochimaru heard the doors to the observation deck whoosh open and he smirked while keeping his eyes on the three figures.

"Ah Margaret, are you here to see the demonstration?" he asked flippantly.

"For your sake you snake, this had better be worth it," Parangosky growled as she walked up beside the man. "Over 99 percent of the test subjects we gave you died. This boy is supposedly the only one to successfully assimilate the DNA?"

"Yes he is. All in all it was exactly within my calculations. While the loss of those other test subjects was tragic, 09's more than made their sacrifice worth it in my opinion," Orochimaru remarked unapologetically. Seeing the look Parangosky was giving him out of the corner of his eye, he continued, "That said, a visual demonstration is always the best demonstration." Turning on a com link he had in his ear, he spoke a single word into it that was relayed over the loud speaker in the sparing area below.

"Hajime!"

With that, the security forces brought out their stun batons and started to advance on Subject 09. However, before they could reach him, the child underwent a startling transformation! First he bulked up in both size and muscle until he was over six feet tall. Then, his skin turned a dark bluish gray color as his hair receded into his scalp. Then his jaw seemed to break apart until it was replaced by four mandibles filled with needle like teeth. His head then lengthened as his legs cracked and became both hooved and double jointed. Where was once a human child now stood a young but deadly Sangheili.

The mutated saurian easily grabbed the wrist of the first guard to approach him and lifted the full grown man up into the air like one would a sack of potatoes. He then hurled the unfortunate man into the onrushing group, knocking three of them over. He then snapped out a hooved foot that caught another guard in their armored chest, causing the padding to become indented as the human went flying into the opposite wall where he lay still. Yet another guard was able to get close to the alien hybrid and whacked him in the ribs with their stun baton. All this seemed to do however, was enrage him. Letting out a roar, the Sangheili started to attack with a speed and ferocity few live to see. Before it had been even ten minutes since they started, the human experiment was the only standing being in the area while the rest of the guards were either out cold or having crippling wounds. With a sigh, the Sangheili shrunk back down into his human form before heading back to where he knew the entrance to his room was, knowing that the experiments were done for the day.

Back with the two observers, Parangosky stood while trying to hide her surprised look. "I'll be damned," she whispered, "I wouldn't have thought it possible until I saw it with my own eyes." Turning to Orochimaru she asked, "And he can turn into other members of the Covenant as well?"

Orochimaru nodded as he eyed his notes. "Yes, we were able to blend 09's DNA with that of Sangheili, Unggoy, different breeds of Kig-Yar, Jiralhanae, and even Yanme'e. Unfortunately we couldn't use Mgalekgolo due to their hive mind bodies, but we should have enough to make the universe's most successful spy. All that remains is to teach him what intel on the Covenant we gathered so he can learn their languages, behavioral patterns, and anything else of importance. Then it is just a matter of finding the best place and time to plant our little mole and then we should expect results almost instantly!"

Nodding, Parangosky said sharply, "See that our weapon will be ready soon. We'll need him if we're ever going to make any headway in this damn war."

With that, she turned around and left towards the elevator. Her departure was so abrupt, the wind caused by it made one of the papers held by Orochimaru to flutter to the floor. On the paper read the following:

 **Operation SNAFU Subject 09**

 **Name:** Naruto Uzumaki-Namikaze

 **Age:** 7 (DOB Oct. 10, 2537)

 **Family:** Kushina Uzumaki-Namikaze (mother, deceased), Minato Uzumaki-Namikaze (father, deceased), Jiraiya Namikaze (adopted grandfather, alive), other familial relations unknown

 **Abilities:** Has DNA of several of the main species in the Covenant spliced with his own DNA. Can take the form of said species and has their strengths and weaknesses when in specific form. Can channel certain aspects while in human form, limited. Shows remarkable amounts of resilience in both the physical and the mental. Possible flight risk? Further testing required.

The Human-Covenant War just got a new player! But will he be humanity's savior…or its destroyer?


End file.
